Workflow

Click the nodes to obtain details about each step.

Read QC

Read Trimming

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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out_dir:
    '/Users/csifuentes/Documents/outDataModularInclude'
input_dir:
    fastq: '/Users/csifuentes/Documents/testData/simulated_reads/fastq'
    genome_fasta: '/Users/csifuentes/Documents/testData/index/'
    genome_gtf: '/Users/csifuentes/Documents/testData/index/Homo_sapiens.GRCh38.103.gtf'
read_info:
    fastq_suffix: 'fastq'
    r1_suffix: '_1' 
thread_info:
    fastqc: 4
    align: 4
    counts: 4
trim_info:
    tool: 'fastp'
    length: 20
    quality: 30
count_info:
    strand: 0
diffex_info:
    prefix: 'WT_vs_KO'
    metadata: '/Users/csifuentes/Documents/repo/Basic-Bulk-RNA-seq-Workflow/workflow_modularized_include/resources/metadata.txt'

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